Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 96 of 292
Found at i:29318432 original size:29 final size:29
Alignment explanation
Indices: 29318399--29318529 Score: 172
Period size: 29 Copynumber: 4.5 Consensus size: 29
29318389 TGACGAGATC
*
29318399 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* *
29318428 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
*
29318457 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* ** *
29318486 GGCACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
**
29318515 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
29318530 AGCTCGGAGG
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 92 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAAAATAT
Found at i:29321912 original size:11 final size:10
Alignment explanation
Indices: 29321880--29321925 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
29321870 CATGAGATTT
29321880 TGATAT-ACA
1 TGATATGACA
*
29321889 TGATTTGACA
1 TGATATGACA
29321899 TGATATGCACA
1 TGATATG-ACA
*
29321910 TGATATG-TA
1 TGATATGACA
29321919 TGATATG
1 TGATATG
29321926 CACGTGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 13 0.41
10 9 0.28
11 10 0.31
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (10 bp):
TGATATGACA
Found at i:29322051 original size:26 final size:26
Alignment explanation
Indices: 29322003--29322075 Score: 121
Period size: 26 Copynumber: 2.8 Consensus size: 26
29321993 CCTAGTTACA
*
29322003 GAAAAGGGC-TTTGCCCCAATTTATC
1 GAAAAGGGCTTTTGCCCCAGTTTATC
29322028 GAAAAGGGCTTTTGCCCCAGTTTATC
1 GAAAAGGGCTTTTGCCCCAGTTTATC
*
29322054 AAAAAGGGCTTTTGCCCCAGTT
1 GAAAAGGGCTTTTGCCCCAGTT
29322076 ATTAAAAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 9 0.20
26 36 0.80
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (26 bp):
GAAAAGGGCTTTTGCCCCAGTTTATC
Found at i:29322077 original size:25 final size:24
Alignment explanation
Indices: 29321980--29322082 Score: 109
Period size: 26 Copynumber: 4.1 Consensus size: 24
29321970 GAGGAAGTGC
* *
29321980 AAAAGGGCTATGCCCTAGTTA-CA
1 AAAAGGGCTTTGCCCCAGTTATCA
* *
29322003 GAAAAGGGCTTTGCCCCAATTTATCG
1 -AAAAGGGCTTTGCCCC-AGTTATCA
29322029 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGC-TTTGCCCCAG-TTATCA
*
29322055 AAAAGGGCTTTTGCCCCAGTTATTA
1 AAAAGGGC-TTTGCCCCAGTTATCA
29322080 AAA
1 AAA
29322083 GAGGCTAGGC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.21
25 21 0.31
26 33 0.49
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTATCA
Found at i:29328814 original size:34 final size:33
Alignment explanation
Indices: 29328737--29328817 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
29328727 TTTATTTGCA
*
29328737 TACTGTACTGAAATGGGATAAGGCCCAGACTAC
1 TACTGTACTGAAATGGGATAAGGCCCAAACTAC
* * * * *
29328770 CACTGTTACTGAAATGGGCTCAGGCCTAAACTGC
1 TACTG-TACTGAAATGGGATAAGGCCCAAACTAC
29328804 TACTGCTACTGAAA
1 TACTG-TACTGAAA
29328818 GAGGGGCTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 4 0.10
34 35 0.90
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (33 bp):
TACTGTACTGAAATGGGATAAGGCCCAAACTAC
Found at i:29331309 original size:50 final size:51
Alignment explanation
Indices: 29331255--29331378 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 51
29331245 TCTCCTTTCT
***
29331255 TTGAAATCATTCATGCTCATGCATTTGAAATGAGAAA-ATGTTC-CTATG-A
1 TTGAAATCATTCATGCTCATGCATTTG-AATGAGAAAGAACATCTCTATGCA
* * * *
29331304 GTTGAAACCATCCATGCTCATGTATTTGAATGATAAAGAACATCTCTATGCA
1 -TTGAAATCATTCATGCTCATGCATTTGAATGAGAAAGAACATCTCTATGCA
29331356 TTGAAATCATTCATGCTTCATGC
1 TTGAAATCATTCATGC-TCATGC
29331379 TTGAAACGTC
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
49 8 0.13
50 27 0.45
51 19 0.32
52 6 0.10
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (51 bp):
TTGAAATCATTCATGCTCATGCATTTGAATGAGAAAGAACATCTCTATGCA
Found at i:29333963 original size:10 final size:10
Alignment explanation
Indices: 29333948--29333977 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
29333938 CTTGATTTAT
29333948 TACACATATA
1 TACACATATA
29333958 TACACATATA
1 TACACATATA
29333968 T-CACATATA
1 TACACATATA
29333977 T
1 T
29333978 TTAAACCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (10 bp):
TACACATATA
Found at i:29339232 original size:43 final size:43
Alignment explanation
Indices: 29339163--29339323 Score: 166
Period size: 43 Copynumber: 3.8 Consensus size: 43
29339153 TGCCCGTACA
* * * * *
29339163 ATGCC-ATATCCCAGATATGGTATTACATGTTATCACGTATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACGTATCG
* * **
29339205 ATGCCAATGTCCCAGACATTGTCTTACACGAAATCATATAAT-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACGT-ATCG
* * *
29339248 ATGCCAATGTCCTAGACATGGTCTTACACATAATCACG-ATACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACGTAT-CG
*
29339291 ATGCCAATGTCCCAGACATGGTCTTACATGTAA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAA
29339324 ACACATCTCG
Statistics
Matches: 96, Mismatches: 19, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
41 2 0.02
42 5 0.05
43 87 0.91
44 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACGTATCG
Found at i:29347650 original size:20 final size:20
Alignment explanation
Indices: 29347603--29347650 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
29347593 TGTAAGCTCG
29347603 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
29347623 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
29347643 GTTGAGCT
1 GTTGAGCT
29347651 GGACGGAGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:29348718 original size:37 final size:37
Alignment explanation
Indices: 29348665--29348767 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
29348655 CGAATAGTCC
*
29348665 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
29348702 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
29348739 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
29348768 ATATATTTCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:29348985 original size:17 final size:17
Alignment explanation
Indices: 29348965--29348997 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29348955 TATCTCATAC
29348965 ATATTTCACACTAGCCG
1 ATATTTCACACTAGCCG
29348982 ATATTTCACACTAGCC
1 ATATTTCACACTAGCC
29348998 ATTCGGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.30
Consensus pattern (17 bp):
ATATTTCACACTAGCCG
Found at i:29348999 original size:65 final size:65
Alignment explanation
Indices: 29348917--29349045 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 65
29348907 GGTCTCCTAC
*
29348917 ATATTTCACAGTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCG
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCG
*
29348982 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTCATATTTCACACTAGCC
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCC
29349046 ATTCGGCTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (65 bp):
ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCG
Found at i:29349015 original size:48 final size:48
Alignment explanation
Indices: 29348982--29349406 Score: 771
Period size: 48 Copynumber: 8.9 Consensus size: 48
29348972 ACACTAGCCG
29348982 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
*
29349030 ATATTTCACACTAGCCATTCGGCTTTACCATATATACATATCTCATTC
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
29349078 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATAT-
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCAT-TC
*
29349126 ATATTTTACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
29349174 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
29349222 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
* *
29349270 ATATTTCACACTAGCCATTCGGCTTTACCCCATATACATATCTCATAC
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
* *
29349318 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATAC
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
*
29349366 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATAT
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATAT
29349407 ATATTTATCT
Statistics
Matches: 367, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
47 1 0.00
48 365 0.99
49 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (48 bp):
ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATTC
Found at i:29349173 original size:28 final size:28
Alignment explanation
Indices: 29349141--29349269 Score: 74
Period size: 28 Copynumber: 5.2 Consensus size: 28
29349131 TTACACTAGC
29349141 CATTCGGCTTTACCACATATACATATCT
1 CATTCGGCTTTACCACATATACATATCT
*** *
29349169 CATTCATATTT--CAC----AC-TAGC-
1 CATTCGGCTTTACCACATATACATATCT
29349189 CATTCGGCTTTACCACATATACATATCT
1 CATTCGGCTTTACCACATATACATATCT
*** *
29349217 CATTCATATTT--CAC----AC-TAGC-
1 CATTCGGCTTTACCACATATACATATCT
29349237 CATTCGGCTTTACCACATATACATATCT
1 CATTCGGCTTTACCACATATACATATCT
29349265 CATTC
1 CATTC
29349270 ATATTTCACA
Statistics
Matches: 69, Mismatches: 16, Indels: 32
0.59 0.14 0.27
Matches are distributed among these distances:
20 16 0.23
21 6 0.09
22 10 0.14
26 10 0.14
27 6 0.09
28 21 0.30
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.36
Consensus pattern (28 bp):
CATTCGGCTTTACCACATATACATATCT
Found at i:29353052 original size:18 final size:19
Alignment explanation
Indices: 29353029--29353067 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
29353019 TTTATCTCAA
*
29353029 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
29353047 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
29353066 TT
1 TT
29353068 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:29353109 original size:24 final size:24
Alignment explanation
Indices: 29353060--29353144 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
29353050 CTTGTTCACA
* * *
29353060 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTTTCTCAATCTCATT
* * *
29353084 TTCGTTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTTTCTCAATCTCATT
**
29353108 TTCTTTTTCACTCTCAATCTCATT
1 TTCTTTTTCTTTCTCAATCTCATT
29353132 TTCTTTTTCTTTC
1 TTCTTTTTCTTTC
29353145 ATTTCTTTGT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.12, C:0.27, G:0.01, T:0.60
Consensus pattern (24 bp):
TTCTTTTTCTTTCTCAATCTCATT
Found at i:29353133 original size:18 final size:18
Alignment explanation
Indices: 29353089--29353134 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29353079 TCTTTTTCGT
*
29353089 TCTCTTTTTCAATCTCAT
1 TCTCTTTTTCAATCTCAA
* *
29353107 TTTCTTTTTCACTCTCAA
1 TCTCTTTTTCAATCTCAA
*
29353125 TCTCATTTTC
1 TCTCTTTTTC
29353135 TTTTTCTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTCTTTTTCAATCTCAA
Found at i:29353173 original size:42 final size:44
Alignment explanation
Indices: 29353138--29353234 Score: 123
Period size: 42 Copynumber: 2.3 Consensus size: 44
29353128 CATTTTCTTT
* *
29353138 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCA--TTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTTTCAAGA
*
29353179 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCA--TTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTTTCAAGA
*
29353221 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
29353235 CTCATAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 7 0.14
42 44 0.86
ACGTcount: A:0.14, C:0.24, G:0.05, T:0.57
Consensus pattern (44 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTTTCAAGA
Found at i:29353212 original size:21 final size:21
Alignment explanation
Indices: 29353145--29353212 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
29353135 TTTTTCTTTC
*
29353145 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
29353166 ATTTCATTCAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
29353186 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
29353208 ATTTC
1 ATTTC
29353213 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:29355692 original size:10 final size:10
Alignment explanation
Indices: 29355673--29355707 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
29355663 AAGTTCGGTT
29355673 GAGCTCAAAC
1 GAGCTCAAAC
*
29355683 GAGCTGAAAC
1 GAGCTCAAAC
*
29355693 GAGCTCAAAT
1 GAGCTCAAAC
29355703 GAGCT
1 GAGCT
29355708 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:29355716 original size:20 final size:20
Alignment explanation
Indices: 29355670--29355717 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29355660 AGTAAGTTCG
29355670 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
29355690 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
29355710 GTTGAGCT
1 GTTGAGCT
29355718 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:29357091 original size:27 final size:27
Alignment explanation
Indices: 29357060--29357265 Score: 202
Period size: 27 Copynumber: 7.7 Consensus size: 27
29357050 GTACATAGAC
* *
29357060 CCCCTTTGTGGTAAAATGATTCTATTG
1 CCCCTTTGTGGTAAAATGATTATTTTG
* *
29357087 CCCCTGTGTGGTAAAATGACTATTTTG
1 CCCCTTTGTGGTAAAATGATTATTTTG
* * * *
29357114 -CCCATTGTGGTAAAATGACTGTATTG
1 CCCCTTTGTGGTAAAATGATTATTTTG
* *
29357140 CCCCTGTGTGGTAAAATGACTATTTTG
1 CCCCTTTGTGGTAAAATGATTATTTTG
* *
29357167 CCCC-TTGTGGTTAAATGATTGTTTTG
1 CCCCTTTGTGGTAAAATGATTATTTTG
* *
29357193 CCCCTATGAGGTAAAATGATTATTTT-
1 CCCCTTTGTGGTAAAATGATTATTTTG
* * *
29357219 TCCCTTATGTGGTGAAATGATTGTTTTG
1 CCCCTT-TGTGGTAAAATGATTATTTTG
* * *
29357247 CCCTTTTATGGTAAGATGA
1 CCCCTTTGTGGTAAAATGA
29357266 CTGTTTTACC
Statistics
Matches: 145, Mismatches: 30, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
26 48 0.33
27 93 0.64
28 4 0.03
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (27 bp):
CCCCTTTGTGGTAAAATGATTATTTTG
Found at i:29357128 original size:53 final size:53
Alignment explanation
Indices: 29357065--29357272 Score: 254
Period size: 53 Copynumber: 3.9 Consensus size: 53
29357055 TAGACCCCCT
*
29357065 TTGTGGTAAAATGATTCTATTGCCCCTGTGTGGTAAAATGACTATTTTGCCCA
1 TTGTGGTAAAATGATTGTATTGCCCCTGTGTGGTAAAATGACTATTTTGCCCA
* *
29357118 TTGTGGTAAAATGACTGTATTGCCCCTGTGTGGTAAAATGACTATTTTGCCCC
1 TTGTGGTAAAATGATTGTATTGCCCCTGTGTGGTAAAATGACTATTTTGCCCA
* * * * * * *
29357171 TTGTGGTTAAATGATTGTTTTGCCCCTATGAGGTAAAATGATTATTTTTCCCT
1 TTGTGGTAAAATGATTGTATTGCCCCTGTGTGGTAAAATGACTATTTTGCCCA
* * * * * * *
29357224 TATGTGGTGAAATGATTGTTTTGCCCTTTTATGGTAAGATGACTGTTTT
1 T-TGTGGTAAAATGATTGTATTGCCCCTGTGTGGTAAAATGACTATTTT
29357273 ACCCTTATGT
Statistics
Matches: 135, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 96 0.71
54 39 0.29
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (53 bp):
TTGTGGTAAAATGATTGTATTGCCCCTGTGTGGTAAAATGACTATTTTGCCCA
Found at i:29357230 original size:80 final size:79
Alignment explanation
Indices: 29357061--29357272 Score: 210
Period size: 80 Copynumber: 2.7 Consensus size: 79
29357051 TACATAGACC
* * *
29357061 CCCTTTGTGGTAAAATGATTCTATTGCCCCTGTGTGGTAAAATGACTATTTTGCCCATTGTGGTA
1 CCCTTTGTGGTAAAATGATTATTTTGCCCCTGTGTGGTAAAATGACTATTTTGCCCATTGAGGTA
*
29357126 AAATGACTGTATTG
66 AAATGACTATATTG
* * * * * *
29357140 CCCCTGTGTGGTAAAATGACTATTTTGCCCCT-TGTGGTTAAATGATTGTTTTGCCCCTATGAGG
1 -CCCTTTGTGGTAAAATGATTATTTTGCCCCTGTGTGGTAAAATGACTATTTTGCCCAT-TGAGG
* * *
29357204 TAAAATGATTATTTTT
64 TAAAATGACTATATTG
* * * * * * *
29357220 CCCTTATGTGGTGAAATGATTGTTTTGCCCTTTTATGGTAAGATGACTGTTTT
1 CCCTT-TGTGGTAAAATGATTATTTTGCCCCTGTGTGGTAAAATGACTATTTT
29357273 ACCCTTATGT
Statistics
Matches: 107, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
79 26 0.24
80 65 0.61
81 16 0.15
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (79 bp):
CCCTTTGTGGTAAAATGATTATTTTGCCCCTGTGTGGTAAAATGACTATTTTGCCCATTGAGGTA
AAATGACTATATTG
Found at i:29358927 original size:23 final size:22
Alignment explanation
Indices: 29358878--29358927 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
29358868 TCTTAACTAC
*
29358878 TCAAATCCATAGCCAAAACATA
1 TCAAATCAATAGCCAAAACATA
*
29358900 CCAAATCAATATGCCAAAA-ATCA
1 TCAAATCAATA-GCCAAAACAT-A
29358923 TCAAA
1 TCAAA
29358928 CTTACATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.52, C:0.26, G:0.04, T:0.18
Consensus pattern (22 bp):
TCAAATCAATAGCCAAAACATA
Found at i:29359759 original size:43 final size:43
Alignment explanation
Indices: 29359660--29359822 Score: 136
Period size: 43 Copynumber: 3.8 Consensus size: 43
29359650 CATAAAGCTC
* * * **
29359660 ATACAATGCC-ATATCCCAGATATGGTGTTACATGTTATCAC-
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGAAATCACG
** * * *
29359701 ATATGGATGCCAATGTCCCAGATATGGTCTCACATGAAATCA-T
1 ATA-CAATGCCAATGTCCCAGACATGGTCTTACATGAAATCACG
* * * *
29359744 ATAACAAT-CCGAATGTCCTAGACAAGGTCTTACACGTAATCACG
1 AT-ACAATGCC-AATGTCCCAGACATGGTCTTACATGAAATCACG
*
29359788 ATACAATGCCAATGTCCCAAACATGGTCTTACATG
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATG
29359823 TAAACACATC
Statistics
Matches: 95, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
41 3 0.03
42 7 0.07
43 80 0.84
44 5 0.05
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (43 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACATGAAATCACG
Found at i:29362298 original size:29 final size:29
Alignment explanation
Indices: 29362216--29362316 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 29
29362206 GCATGAATGT
* * * *
29362216 AATGTGATTTGGGACGGATGGGCCATATA
1 AATGTGAATTGGGCCTGATGGGCCATATG
* * *
29362245 AATGAG-ACTGGGCCTAATGGGCCATATG
1 AATGTGAATTGGGCCTGATGGGCCATATG
*
29362273 AATGTGAATTGGGCCTGATGGTCCATATG
1 AATGTGAATTGGGCCTGATGGGCCATATG
* *
29362302 AACGTGAATAGGGCC
1 AATGTGAATTGGGCC
29362317 ATATAAATGA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 21 0.36
29 37 0.64
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.25
Consensus pattern (29 bp):
AATGTGAATTGGGCCTGATGGGCCATATG
Found at i:29364081 original size:56 final size:54
Alignment explanation
Indices: 29363987--29364099 Score: 131
Period size: 56 Copynumber: 2.1 Consensus size: 54
29363977 TGAAAAAAAA
29363987 AAAGAAAAAAAAAATGTTCATCCTTCTCCATAGGCTTGGCCG-AATGTACTAAGG
1 AAAGAAAAAAAAAATGTTCATCCTTCTCCATAGGCTTGGCCGAAAT-TACTAAGG
* *** *
29364041 AAAGAAAAGAAAAATTTGTTCATCCTT-TCTCATCTTCTTGGCCGAAATTACTAGGG
1 AAAGAAAA-AAAAA-ATGTTCATCCTTCTC-CATAGGCTTGGCCGAAATTACTAAGG
29364097 AAA
1 AAA
29364100 AGGGGGAGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
54 8 0.16
55 7 0.14
56 32 0.64
57 3 0.06
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (54 bp):
AAAGAAAAAAAAAATGTTCATCCTTCTCCATAGGCTTGGCCGAAATTACTAAGG
Found at i:29365372 original size:40 final size:40
Alignment explanation
Indices: 29365290--29365456 Score: 146
Period size: 40 Copynumber: 4.2 Consensus size: 40
29365280 AAATTGAATG
* * ** *
29365290 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTGACT
* *
29365329 ATATCCGGG-TCAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCT-AAGACCCGAAGGCAATTGTGCGAGTGACT
* * *
29365369 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGACT
* * *
29365409 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGACT
29365449 ATATCCGG
1 ATATCCGG
29365457 TTATATTCCG
Statistics
Matches: 104, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
38 1 0.01
39 16 0.15
40 84 0.81
41 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACT
Found at i:29373333 original size:40 final size:40
Alignment explanation
Indices: 29373274--29373460 Score: 180
Period size: 40 Copynumber: 4.7 Consensus size: 40
29373264 CATTGGAATG
* * * *
29373274 ATATCCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTATT
* *
29373314 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTTATT
* **
29373354 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTATT
* * * * *
29373394 AAATCCGGGTTAAGACCCGAAGGCAATCGTGCGAA-TCACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTATT
* * * *
29373434 ATAACCGGGCTAGGTCCCGAAGACAAT
1 ATATCCGGGCTAAGACCCGAAGGCAAT
29373461 CGAGCGAGTC
Statistics
Matches: 122, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.94
41 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTATT
Found at i:29373408 original size:80 final size:80
Alignment explanation
Indices: 29373274--29373427 Score: 218
Period size: 80 Copynumber: 1.9 Consensus size: 80
29373264 CATTGGAATG
* * ** *
29373274 ATATCCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCA
*
29373339 TTCGTGCGAGTTGTT
66 ATCGTGCGAGTTGTT
* * * *
29373354 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCA
29373419 ATCGTGCGA
66 ATCGTGCGA
29373428 ATCACTATAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 64 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCA
ATCGTGCGAGTTGTT
Found at i:29373442 original size:80 final size:80
Alignment explanation
Indices: 29373278--29373460 Score: 213
Period size: 80 Copynumber: 2.3 Consensus size: 80
29373268 GGAATGATAT
* ** * *
29373278 CCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGTCCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCAATCG
* *** *
29373343 TGCGAGTTGTTATAT
66 TGCGAATCACTATAA
* * * * *
29373358 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATCG
1 CCGGGCTAAGTCCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCAATCG
29373423 TGCGAATCACTATAA
66 TGCGAATCACTATAA
* *
29373438 CCGGGCTAGGTCCCGAAGACAAT
1 CCGGGCTAAGTCCCGAAGGCAAT
29373461 CGAGCGAGTC
Statistics
Matches: 84, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.21
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCAATCG
TGCGAATCACTATAA
Found at i:29373480 original size:80 final size:80
Alignment explanation
Indices: 29373278--29373495 Score: 181
Period size: 80 Copynumber: 2.7 Consensus size: 80
29373268 GGAATGATAT
* * * * * * * *
29373278 CCGGGCTAAGTCCCGAAGGCAAT-TATGCTAGTAATTATATCCGGGCTAAGACCCGAAGGCATTC
1 CCGGGCTAAGACCCGAAGACAATCGA-GCAAGTCACTATATCCGGGTTAAGACCCGAAGGCAATC
* *** *
29373342 GTGCGAGTTGTTATAT
65 GTGCGAATCACTATAA
* * * * * * *
29373358 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATCG
1 CCGGGCTAAGACCCGAAGACAATCGAGCAAGTCACTATATCCGGGTTAAGACCCGAAGGCAATCG
29373423 TGCGAATCACTATAA
66 TGCGAATCACTATAA
* * * *
29373438 CCGGGCTAGGTCCCGAAGACAATCGAGCGAGTCGCTATATCC-GGTTAA-ATCCCGAAGG
1 CCGGGCTAAGACCCGAAGACAATCGAGCAAGTCACTATATCCGGGTTAAGA-CCCGAAGG
29373496 TACGTGATTC
Statistics
Matches: 109, Mismatches: 27, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
78 1 0.01
79 14 0.13
80 94 0.86
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGACAATCGAGCAAGTCACTATATCCGGGTTAAGACCCGAAGGCAATCG
TGCGAATCACTATAA
Found at i:29378788 original size:44 final size:44
Alignment explanation
Indices: 29378725--29378813 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
29378715 ATATATGTGT
*
29378725 AGCCAAGCTACCACATAACCCACCCATGAGTGAACTCGGACTCA
1 AGCCAAGCTACCACATAACCCACCCATAAGTGAACTCGGACTCA
**
29378769 AGCCAAGCTACCATGTAACCCACCCATAAGTGAACTCGGACTCA
1 AGCCAAGCTACCACATAACCCACCCATAAGTGAACTCGGACTCA
29378813 A
1 A
29378814 CTCAACGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.35, C:0.35, G:0.16, T:0.15
Consensus pattern (44 bp):
AGCCAAGCTACCACATAACCCACCCATAAGTGAACTCGGACTCA
Found at i:29398046 original size:36 final size:36
Alignment explanation
Indices: 29398004--29398157 Score: 112
Period size: 40 Copynumber: 4.1 Consensus size: 36
29397994 GAAGACATTT
* * *
29398004 ATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGC
1 ATGCTAGTAACTACATCCGGGCTAAGACCCGAAGGC
*
29398040 ATGCTAGTGACTACATCCGGGCTAAGACCCGAAGGC
1 ATGCTAGTAACTACATCCGGGCTAAGACCCGAAGGC
* *** *
29398076 ATTCGTGCAAGTTGTTAAATCCGGGCTAAGACCCGAAGGC
1 A----TGCTAGTAACTACATCCGGGCTAAGACCCGAAGGC
* * *
29398116 ATTCGT-GCAAGTCGTTAAATCCGGGCTAAGACCCGAAGGC
1 ATGC-TAGTAA--C--TACATCCGGGCTAAGACCCGAAGGC
29398156 AT
1 AT
29398158 TCGTGCACGT
Statistics
Matches: 94, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
36 36 0.38
40 58 0.62
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (36 bp):
ATGCTAGTAACTACATCCGGGCTAAGACCCGAAGGC
Found at i:29398109 original size:40 final size:40
Alignment explanation
Indices: 29398054--29398179 Score: 216
Period size: 40 Copynumber: 3.1 Consensus size: 40
29398044 TAGTGACTAC
*
29398054 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTAA
29398094 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTAA
* * *
29398134 ATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGGTTAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTAA
29398174 ATCCGG
1 ATCCGG
29398180 TTGTATTCCG
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTAA
Found at i:29414921 original size:28 final size:28
Alignment explanation
Indices: 29414890--29414956 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
29414880 GCCATTTCAT
29414890 ATATGTTGCATACATGCATGATATTATG
1 ATATGTTGCATACATGCATGATATTATG
29414918 ATATGTTGCATACATGCATGATATTATG
1 ATATGTTGCATACATGCATGATATTATG
29414946 ATATGTTGCAT
1 ATATGTTGCAT
29414957 GGGGATAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (28 bp):
ATATGTTGCATACATGCATGATATTATG
Found at i:29417806 original size:40 final size:40
Alignment explanation
Indices: 29417740--29417906 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
29417730 AAATTGAATG
* * * *
29417740 ATATCCGGGCTAA-TCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
29417779 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
29417819 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
29417859 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
29417899 ATATCCGG
1 ATATCCGG
29417907 TTATATTCCG
Statistics
Matches: 104, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
39 15 0.14
40 87 0.84
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:29425812 original size:40 final size:40
Alignment explanation
Indices: 29425746--29425912 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
29425736 AAATTGAATG
* * * *
29425746 ATATCCGGGCTAA-TCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
29425785 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
29425825 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
29425865 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
29425905 ATATCCGG
1 ATATCCGG
29425913 TTATATTCCG
Statistics
Matches: 104, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
39 15 0.14
40 87 0.84
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:29429231 original size:30 final size:30
Alignment explanation
Indices: 29429197--29429257 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29429187 TCCTTAACTC
29429197 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
29429227 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
29429257 A
1 A
29429258 GGCTTGGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:29435961 original size:40 final size:40
Alignment explanation
Indices: 29435902--29435989 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
29435892 CAATTGAATG
* *
29435902 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCGCGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTCGTT
* *
29435942 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTCGTT
29435982 ATATCCGG
1 ATATCCGG
29435990 TTGTATTCCG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCACGTCGTT
Found at i:29443041 original size:40 final size:40
Alignment explanation
Indices: 29442875--29443042 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
29442865 CATTTGAATG
* * *
29442875 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
29442915 ATGTCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * * **
29442955 ATATCCGGGCTAAGACCCGAAGGCAATGGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
29442995 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
29443035 GTATCCGG
1 ATATCCGG
29443043 TTAAATCCGA
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.03
40 95 0.93
41 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:29450074 original size:40 final size:40
Alignment explanation
Indices: 29449908--29450075 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
29449898 CATTTGAATG
* * *
29449908 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
29449948 ATGTCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * * **
29449988 ATATCCGGGCTAAGACCCGAAGGCAATGGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
29450028 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
29450068 GTATCCGG
1 ATATCCGG
29450076 TTAAATCCGA
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.03
40 95 0.93
41 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:29458054 original size:40 final size:40
Alignment explanation
Indices: 29457888--29458055 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
29457878 CATTTGAATG
* * *
29457888 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
29457928 ATGTCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * * **
29457968 ATATCCGGGCTAAGACCCGAAGGCAATGGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
29458008 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
29458048 GTATCCGG
1 ATATCCGG
29458056 TTAAATCCCG
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.03
40 95 0.93
41 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:29461453 original size:12 final size:12
Alignment explanation
Indices: 29461436--29461461 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29461426 AGGTATTACC
29461436 CGTGTTCCACAT
1 CGTGTTCCACAT
29461448 CGTGTTCCACAT
1 CGTGTTCCACAT
29461460 CG
1 CG
29461462 AGCTGTAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.19, T:0.31
Consensus pattern (12 bp):
CGTGTTCCACAT
Found at i:29462078 original size:12 final size:12
Alignment explanation
Indices: 29462061--29462087 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29462051 ATGTCAAATT
29462061 CAATGGCTTATA
1 CAATGGCTTATA
29462073 CAATGGCTTATA
1 CAATGGCTTATA
29462085 CAA
1 CAA
29462088 AATAATTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (12 bp):
CAATGGCTTATA
Found at i:29463378 original size:68 final size:68
Alignment explanation
Indices: 29463228--29463385 Score: 160
Period size: 68 Copynumber: 2.3 Consensus size: 68
29463218 CTAGCCAGTT
* * *
29463228 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
**
29463293 TTTA
65 CATA
* * *
29463297 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
29463359 CTACATA
63 C-ACATA
*
29463366 GTATCTCGTAGCTTTCTTGT
1 -TATCTCGTAGCTCTCTTGT
29463386 ACACATGATG
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
68 35 0.47
69 7 0.09
70 6 0.08
71 26 0.35
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:29463827 original size:31 final size:33
Alignment explanation
Indices: 29463792--29463855 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
29463782 GATTATGTAG
29463792 AAAGAATAAAGAA-ATGAA-AAAAA-AAAGAAAA
1 AAAGAA-AAAGAATATGAAGAAAAACAAAGAAAA
*
29463823 AAAGAAAGAGAATATGAAGAAAAACAAAGAAAA
1 AAAGAAAAAGAATATGAAGAAAAACAAAGAAAA
29463856 GGAAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 5 0.17
31 11 0.38
32 5 0.17
33 8 0.28
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.06
Consensus pattern (33 bp):
AAAGAAAAAGAATATGAAGAAAAACAAAGAAAA
Found at i:29465129 original size:29 final size:29
Alignment explanation
Indices: 29465028--29465121 Score: 161
Period size: 29 Copynumber: 3.2 Consensus size: 29
29465018 GTGACGAGAT
*
29465028 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
29465057 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
29465086 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
29465115 CGGCACT
1 TGGCACT
29465122 GGGTGTGCGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:29472749 original size:34 final size:34
Alignment explanation
Indices: 29472710--29472775 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
29472700 GACAGAGTTA
*
29472710 AAGGAGTTGAAAGTTCAGTTACAAGAGTTGACGG
1 AAGGAGTTGAAAGTTCAATTACAAGAGTTGACGG
29472744 AAGGAGTTGAAAGTTCAATTACAAGAGTTGAC
1 AAGGAGTTGAAAGTTCAATTACAAGAGTTGAC
29472776 ATATAAAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.29, T:0.24
Consensus pattern (34 bp):
AAGGAGTTGAAAGTTCAATTACAAGAGTTGACGG
Found at i:29475219 original size:55 final size:53
Alignment explanation
Indices: 29475117--29475357 Score: 183
Period size: 55 Copynumber: 4.5 Consensus size: 53
29475107 GTTTAAGGAG
* * * *
29475117 ACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCATGGAT
1 ACCATGTAAGACCATGTCAAGACATGG-CATTGATAA-G-TTCATAAGGCATGGAT
* *
29475172 ACCATTTAAGACCATGTCAATACATGGCATTGATAAGTTACTATAAGGCAAAT-G-T
1 ACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-C-ATAAGGC--ATGGAT
* * * * * *
29475227 CCCATGTAAGACCATGCCAAGGCATGGCATTGCTGAGTTCATAAGGCAAGGAT
1 ACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCATAAGGCATGGAT
* * * *
29475280 ATCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTCA-AA---A-GGAT
1 ACCATGTAAGACCATGTCAAGACATGGCATTGATAAG-TTCATAAGGCATGGAT
* * *
29475329 ACCACGTAAGACCATGACAAGTCATGGCA
1 ACCATGTAAGACCATGTCAAGACATGGCA
29475358 ATGGTAGGGT
Statistics
Matches: 151, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
49 28 0.19
50 1 0.01
51 1 0.01
52 3 0.02
53 41 0.27
54 12 0.08
55 62 0.41
56 1 0.01
57 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (53 bp):
ACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCATAAGGCATGGAT
Found at i:29475317 original size:108 final size:110
Alignment explanation
Indices: 29475118--29475318 Score: 282
Period size: 108 Copynumber: 1.8 Consensus size: 110
29475108 TTTAAGGAGA
* * *
29475118 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCATGGATACCATTTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGCTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
* *
29475183 CCATGTCAATACATGGCATTGATAAGTTACTATAAGGCAAATGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAATGTC
* * *
29475228 CCATGTAAGACCATGCCAAGGCATGG-CATTGCTGA-G-TTCATAAGGCAAGGATATCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGCTAAGGTTTC-TAAGGCAAGGATACCATGTAAG
* *
29475290 ACCATGTCGAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
29475319 TCAAAAGGAT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.04
108 45 0.56
109 6 0.08
110 26 0.32
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGCTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAATGTC
Found at i:29483733 original size:16 final size:15
Alignment explanation
Indices: 29483692--29483738 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
29483682 CACTAGGAAT
*
29483692 TATGTGATTATGAGA
1 TATGTGATTATGTGA
29483707 TCATG-GAATTATGTGTA
1 T-ATGTG-ATTATGTG-A
29483724 TATGTGATTATGTGA
1 TATGTGATTATGTGA
29483739 ATCTGGGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 3 0.11
16 21 0.78
17 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.43
Consensus pattern (15 bp):
TATGTGATTATGTGA
Found at i:29484617 original size:20 final size:19
Alignment explanation
Indices: 29484584--29484622 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
29484574 GAGATGTGTG
29484584 ATGAATGACACATGTGCTAA
1 ATGAATGACACATG-GCTAA
29484604 ATGAATGA-ATCATGGCTAA
1 ATGAATGACA-CATGGCTAA
29484623 TAAGTATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (19 bp):
ATGAATGACACATGGCTAA
Found at i:29485317 original size:10 final size:10
Alignment explanation
Indices: 29485282--29485330 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
29485272 CCAAAATAAG
*
29485282 AAAGTTTTCT
1 AAAGTTCTCT
*
29485292 -AAGTTTTCT
1 AAAGTTCTCT
29485301 CAAAGTTCTCT
1 -AAAGTTCTCT
29485312 AAAGTTCTCT
1 AAAGTTCTCT
29485322 AAAGTTCTC
1 AAAGTTCTC
29485331 GGCTTAGTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
9 9 0.25
10 19 0.53
11 8 0.22
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (10 bp):
AAAGTTCTCT
Found at i:29492346 original size:49 final size:46
Alignment explanation
Indices: 29492249--29492464 Score: 161
Period size: 49 Copynumber: 4.6 Consensus size: 46
29492239 AAATGCTGAC
* * * *
29492249 GCCATGTCCCAGACATGGTCTTACACT-AGCTAGCACATCAAAGTCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGA-CT-TCTCATCAAGGCCGAT
*
29492297 GCCATGTCCCAAACAGGTCTTACACTGACTTTCATACATCAAGGCCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGAC-TTC-T-CATCAAGGCCGAT
*** * * * * *
29492346 GTTGTGTCCTAGACAGGTCTTACACTGGCTCTGGTCTATC-GGTGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGACT-T-CTC-ATCAAG-GCCGAT
* * * *
29492395 GCCATGTCCTAGACAGGTCTTACACTGAC-ACTCAACAA-GCTGAT
1 GCCATGTCCCAGACAGGTCTTACACTGACTTCTCATCAAGGCCGAT
29492439 GCCATGTCCCAGACAGGTCTTACACT
1 GCCATGTCCCAGACAGGTCTTACACT
29492465 AGCTTATATA
Statistics
Matches: 134, Mismatches: 25, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
44 29 0.22
45 2 0.01
46 2 0.01
47 13 0.10
48 19 0.14
49 69 0.51
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (46 bp):
GCCATGTCCCAGACAGGTCTTACACTGACTTCTCATCAAGGCCGAT
Found at i:29494953 original size:27 final size:27
Alignment explanation
Indices: 29494923--29494976 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
29494913 AGACACATAG
29494923 AAACAAACTCCAAAATGTCTCTTTTCA
1 AAACAAACTCCAAAATGTCTCTTTTCA
*
29494950 AAACAAACTTCAAAATGTCTCTTTTCA
1 AAACAAACTCCAAAATGTCTCTTTTCA
29494977 TTCTCGACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.31
Consensus pattern (27 bp):
AAACAAACTCCAAAATGTCTCTTTTCA
Found at i:29510079 original size:35 final size:35
Alignment explanation
Indices: 29510033--29510105 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
29510023 GGACTTGGAG
*
29510033 TGTTAGAGCGAAATTTTATTTATAACTCAACTTTA
1 TGTTAGAGCGAAATTTTAGTTATAACTCAACTTTA
29510068 TGTTAGAGCGAAATTTTAGTTATAACTCAACTTTA
1 TGTTAGAGCGAAATTTTAGTTATAACTCAACTTTA
29510103 TGT
1 TGT
29510106 AAAAGATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (35 bp):
TGTTAGAGCGAAATTTTAGTTATAACTCAACTTTA
Found at i:29511527 original size:43 final size:43
Alignment explanation
Indices: 29511462--29511715 Score: 373
Period size: 43 Copynumber: 5.9 Consensus size: 43
29511452 ACATATCATT
* * *
29511462 TCACCGGCATTACGCCTACTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
** * *
29511505 TCACCGATATGAAGCCTGCTAGGCACAAAGGCCTGAATACACA
1 TCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
29511548 TCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* * *
29511591 TCATCGGCACGAAGCCTGCTAGGCACGAAAGCCCGAATACACA
1 TCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* * * *
29511634 TCATCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAACACACA
1 TCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
29511677 TCAACGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATA
1 TCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATA
29511716 TAACACCAGC
Statistics
Matches: 190, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 190 1.00
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.13
Consensus pattern (43 bp):
TCACCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:29511750 original size:38 final size:38
Alignment explanation
Indices: 29511708--29511815 Score: 117
Period size: 38 Copynumber: 2.8 Consensus size: 38
29511698 GGCACGAAGG
* * *
29511708 CCCGAATATAACACCAGCACTAGGCCTGTGGGATTTAT
1 CCCGAATATAACACCAGCACGAAGCCTGCGGGATTTAT
* *
29511746 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAACACCAGCACGAAGCCTGCGGGATTTAT
* * *** *
29511784 CCTGGATATTTTACCAGCAAGAAGCCTGCGGG
1 CCCGAATATAACACCAGCACGAAGCCTGCGGG
29511816 TCTTTAAGCC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (38 bp):
CCCGAATATAACACCAGCACGAAGCCTGCGGGATTTAT
Found at i:29514197 original size:29 final size:29
Alignment explanation
Indices: 29514164--29514295 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
29514154 GTGACGAGAT
*
29514164 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* *
29514193 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * ***
29514222 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * * *
29514251 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ACA
29514280 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
29514296 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATACA
Found at i:29521929 original size:29 final size:29
Alignment explanation
Indices: 29521896--29522027 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
29521886 GTGACGAGAT
*
29521896 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* *
29521925 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * ***
29521954 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * * *
29521983 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ACA
29522012 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
29522028 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATACA
Found at i:29523779 original size:2 final size:2
Alignment explanation
Indices: 29523767--29523803 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
29523757 CACTTTCAAA
29523767 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29523804 TCAACTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29525545 original size:209 final size:209
Alignment explanation
Indices: 29525185--29525607 Score: 792
Period size: 209 Copynumber: 2.0 Consensus size: 209
29525175 TTATTTGGCC
29525185 ACTACAATTTGGCCTATAGCATTTTCAAAAATTTTCACATAGGTCCTATTTCATAATTTTACTCT
1 ACTACAATTTGGCCTATAGCATTTTCAAAAATTTTCACATAGGTCCTATTTCATAATTTTACTCT
29525250 CAAATGACAAAATCAAAGCATGAAATTTTCACACATGCACTTTCACATATAATAAACACAGAATA
66 CAAATGACAAAATCAAAGCATGAAATTTTCACACATGCACTTTCACATATAATAAACACAGAATA
*
29525315 TAACATTTAATTATTTTTGTGACTCGGTTTTGTGATCCCAAAACCACTTTCCAACTAGGGCCAAA
131 TAACATTTAATTATTTTTGTGACTCGATTTTGTGATCCCAAAACCACTTTCCAACTAGGGCCAAA
*
29525380 TTAGGGCTGTCACA
196 TTAGGACTGTCACA
*
29525394 ACTACAATTTGGCCTATAGCATTTTCAGAAATTTTCACATAGGTCCTATTTCATAATTTTACTCT
1 ACTACAATTTGGCCTATAGCATTTTCAAAAATTTTCACATAGGTCCTATTTCATAATTTTACTCT
29525459 CAAATGACAAAATCAAAGCATGAAATTTTCACACATGCACTTTCACATATAATAAACACAGAATA
66 CAAATGACAAAATCAAAGCATGAAATTTTCACACATGCACTTTCACATATAATAAACACAGAATA
* *
29525524 TAACATTTAATTATTTTTGTGACTCGATTTTGTGATCCCGAAACCACTTTCCTACTAGGGCCAAA
131 TAACATTTAATTATTTTTGTGACTCGATTTTGTGATCCCAAAACCACTTTCCAACTAGGGCCAAA
29525589 TTAGGACTGTCACA
196 TTAGGACTGTCACA
*
29525603 CCTAC
1 ACTAC
29525608 GGTACAAGGA
Statistics
Matches: 208, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
209 208 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (209 bp):
ACTACAATTTGGCCTATAGCATTTTCAAAAATTTTCACATAGGTCCTATTTCATAATTTTACTCT
CAAATGACAAAATCAAAGCATGAAATTTTCACACATGCACTTTCACATATAATAAACACAGAATA
TAACATTTAATTATTTTTGTGACTCGATTTTGTGATCCCAAAACCACTTTCCAACTAGGGCCAAA
TTAGGACTGTCACA
Found at i:29533688 original size:44 final size:44
Alignment explanation
Indices: 29533622--29534378 Score: 825
Period size: 44 Copynumber: 17.2 Consensus size: 44
29533612 GGCGAATCCG
* * *
29533622 GCAGATTTGGTATCTCTATATTGACAGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* ** *
29533666 GCAGATTTGGCGTCTCTGTATTGGTGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
29533710 GCAGATTTGGCATCTCTGTATTGGCGGAGAGCAAATCAAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * * * * * * * *
29533754 ACTGATTTGGCGTCTCTGTATTGCCTGAGGGCAAATTGAAAAATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCG-AAGATA
* * * *
29533799 GCAGATTTAGCGTCTCTGTATTGGCAGAGACCAGATCAAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* ** *
29533843 GCAGATTTGGCATCTCTGTGTTGATAGAGAGTAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * * * *
29533887 ACAGATTTGGCGTCCCTGTATTGGCGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * * *
29533931 GCAGGTTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAAATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * * * * *
29533975 GCAGATTTGGCATCTCTGTATTGTCAGAGGGAAAATTGAAAAATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCG-AAGATA
** * *
29534020 ATAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
29534064 GTAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * * * *
29534108 ACAGATTTGGCGTTTCTGTATTGGCAGGGAGCAGATCAAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * * *
29534152 GTAGATTTGGCGA-CTCTGTATTGTCAGAGGGCAGATCAAAGATA
1 GCAGATTTGGC-ATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* ** *
29534196 GCAGATTTGGCGTCTCTGTGCTGACAGAGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
29534240 GCAGATTTGGCGTCTTTGTATTGGCAGGGAGCAGATCGAAGATA
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* *
29534284 GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGAT-
1 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
* * *
29534327 GACAGATTTGGCATCTTTGTATTGGCAGAGAGCAGATCAAAAATA
1 G-CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
*
29534372 ACAGATT
1 GCAGATT
29534379 GGTGTTCCCG
Statistics
Matches: 591, Mismatches: 116, Indels: 12
0.82 0.16 0.02
Matches are distributed among these distances:
43 1 0.00
44 522 0.88
45 68 0.12
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (44 bp):
GCAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATA
Found at i:29534013 original size:221 final size:221
Alignment explanation
Indices: 29533622--29534378 Score: 1045
Period size: 221 Copynumber: 3.4 Consensus size: 221
29533612 GGCGAATCCG
* * * *
29533622 GCAGATTTGGTATCTCTATATTGACAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTAT
1 GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAT
* * * *
29533687 TGGTGGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGGCGGAGAGCAAATCAAAGA
66 TGGCGGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCAAAGA
* * * * *
29533752 TAACTGATTTGGCGTCTCTGTATTGCCTGAGGGCAAATTGAAAAATAGCAGATTTAGCGTCTCTG
131 TAGCAGATTTGGCGTCTCTGTATTGACAGAGGGCAAATTGAAAAATAGCAGATTTGGCGTCTCTG
*
29533817 TATTGGCAGAGACCAGATCAAAGATA
196 TATTGGCAGAGAGCAGATCAAAGATA
* * *
29533843 GCAGATTTGGCATCTCTGTGTTGATAGAGAGTAGATCGAAGATAACAGATTTGGCGTCCCTGTAT
1 GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAT
* *
29533908 TGGCGGAGAGCAGATCAAAGATAGCAGGTTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAA-
66 TGGCGGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGACAGAGAGCAGATC-AAAG
* * * ** *
29533972 ATAGCAGATTTGGCATCTCTGTATTGTCAGAGGGAAAATTGAAAAATAATAGATTTGGCATCTCT
130 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGGGCAAATTGAAAAATAGCAGATTTGGCGTCTCT
*
29534037 GTATTGGCGGAGAGCAGATCAAAGATA
195 GTATTGGCAGAGAGCAGATCAAAGATA
* *
29534064 GTAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATAACAGATTTGGCGTTTCTGTAT
1 GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAT
* * *
29534129 TGGCAGG-GAGCAGATCAAAGATAGTAGATTTGGCGA-CTCTGTATTGTCAGAGGGCAGATCAAA
66 TGGC-GGAGAGCAGATCAAAGATAGCAGATTTGGC-ATCTCTGTATTGACAGAGAGCAGATCAAA
** * * * * *
29534192 GATAGCAGATTTGGCGTCTCTGTGCTGACAGAGAGCAGATCG-AAGATAGCAGATTTGGCGTCTT
129 GATAGCAGATTTGGCGTCTCTGTATTGACAGAGGGCAAATTGAAAAATAGCAGATTTGGCGTCTC
* *
29534256 TGTATTGGCAGGGAGCAGATCGAAGATA
194 TGTATTGGCAGAGAGCAGATCAAAGATA
* * *
29534284 GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATGACAGATTTGGCATCTTTGTAT
1 GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAT
* * *
29534349 TGGCAGAGAGCAGATCAAAAATAACAGATT
66 TGGCGGAGAGCAGATCAAAGATAGCAGATT
29534379 GGTGTTCCCG
Statistics
Matches: 471, Mismatches: 60, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
219 1 0.00
220 129 0.27
221 335 0.71
222 6 0.01
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (221 bp):
GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAT
TGGCGGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCAAAGA
TAGCAGATTTGGCGTCTCTGTATTGACAGAGGGCAAATTGAAAAATAGCAGATTTGGCGTCTCTG
TATTGGCAGAGAGCAGATCAAAGATA
Found at i:29542191 original size:25 final size:23
Alignment explanation
Indices: 29542163--29542247 Score: 89
Period size: 26 Copynumber: 3.4 Consensus size: 23
29542153 CTGGAGGCCT
*
29542163 AGCCTCTTTTTATAACTGGGGCAAA
1 AGCC-CTTTTTA-AACTGGGGCATA
*
29542188 AGCCCTTTCGGTAAACTGGGGCATA
1 AGCCCTTT--TTAAACTGGGGCATA
29542213 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTT---TAAACTGGGGCATA
29542239 AGCCCTTTT
1 AGCCCTTTT
29542248 GCACTTCCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.08
25 23 0.44
26 25 0.48
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
AGCCCTTTTTAAACTGGGGCATA
Found at i:29542229 original size:26 final size:26
Alignment explanation
Indices: 29542176--29542247 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
29542166 CTCTTTTTAT
*
29542176 AACTGGGGCAAAAGCCC-TTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
29542201 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
29542227 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
29542248 GCACTTCCTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 16 0.36
26 29 0.64
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:29542324 original size:20 final size:20
Alignment explanation
Indices: 29542296--29542390 Score: 115
Period size: 20 Copynumber: 4.8 Consensus size: 20
29542286 TTATGAATAC
* *
29542296 ATCACGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
29542316 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
29542336 ATCATGTGCATTTTATACAT
1 ATCATGTGCATATCATACAT
*
29542356 GTCATGTGCATATCATACCA-
1 ATCATGTGCATATCATA-CAT
29542376 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
29542391 TCCCATGTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.12
20 56 0.85
21 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29542346 original size:40 final size:40
Alignment explanation
Indices: 29542296--29542382 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
29542286 TTATGAATAC
*
29542296 ATCACGTGCATTTCATACATATCATGTGCATATCATA-CA
1 ATCATGTGCATTTCATACATATCATGTGCATATCATACCA
* *
29542335 TATCATGTGCATTTTATACATGTCATGTGCATATCATACCA
1 -ATCATGTGCATTTCATACATATCATGTGCATATCATACCA
29542376 ATCATGT
1 ATCATGT
29542383 ATATCATATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 41 0.95
41 2 0.05
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (40 bp):
ATCATGTGCATTTCATACATATCATGTGCATATCATACCA
Found at i:29545661 original size:93 final size:93
Alignment explanation
Indices: 29545548--29545716 Score: 293
Period size: 93 Copynumber: 1.8 Consensus size: 93
29545538 CCATAAGCGA
* *
29545548 ACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
29545613 ACTTCGGATGCCTAGTTACATCTCACGG
66 ACTTCGGATGCCTAGTTACATCTCACGG
* *
29545641 ACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
*
29545706 AGTTCGGATGC
66 ACTTCGGATGC
29545717 TCAACCATCC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
ACTTCGGATGCCTAGTTACATCTCACGG
Found at i:29545713 original size:46 final size:46
Alignment explanation
Indices: 29545538--29545713 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
29545528 TGTAACCCGC
* * * * *
29545538 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
29545584 CCATAAGTGAACTCGGACTCAACTCAACGACTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
29545634 -C-TCACG-G-ACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCAT-AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
29545677 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
29545714 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 11, Indels: 22
0.77 0.08 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 4 0.04
45 2 0.02
46 59 0.55
47 26 0.24
48 2 0.02
49 4 0.04
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:29545732 original size:46 final size:46
Alignment explanation
Indices: 29545587--29545725 Score: 128
Period size: 47 Copynumber: 3.0 Consensus size: 46
29545577 TTCGCATCCA
*
29545587 TAAGTGAACTCGGACTCAACTCAACGACTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * *
29545635 TCACG-G-ACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 T-AAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
29545680 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
29545726 CTAGTGACAT
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
44 10 0.14
45 2 0.03
46 26 0.35
47 27 0.36
48 2 0.03
49 6 0.08
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:29556256 original size:40 final size:39
Alignment explanation
Indices: 29556168--29556351 Score: 140
Period size: 40 Copynumber: 4.6 Consensus size: 39
29556158 AAATTGAATG
* * * *
29556168 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGCAA-T-TG-TGCAAGTCGT
* * * *
29556208 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTCG-T
* *
29556248 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTC-GT
* * *
29556288 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTCGT
* * *
29556327 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
29556352 CTTGGTGCGG
Statistics
Matches: 116, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
37 4 0.03
38 2 0.02
39 5 0.04
40 103 0.89
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTCGT
Found at i:29556376 original size:80 final size:81
Alignment explanation
Indices: 29556208--29556396 Score: 195
Period size: 80 Copynumber: 2.4 Consensus size: 81
29556198 GCTGGAAATT
* * * *
29556208 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTATATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTATATCCGGGCTAAGACCCGAAGGCA
*
29556273 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * *
29556289 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ATATCCGGGCTAAGACCCGAAGGC
* * * *
29556352 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
29556368 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
29556397 AACGAGTAGC
Statistics
Matches: 87, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
79 2 0.02
80 85 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:29564282 original size:40 final size:38
Alignment explanation
Indices: 29564233--29564366 Score: 135
Period size: 40 Copynumber: 3.4 Consensus size: 38
29564223 TGCTGGAAAT
* * *
29564233 TATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AGTCG
*
29564272 CTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCAT
1 -TATATCCGGGCTAAGACCCGAAGGCAATT-GTGC-AGTC-G
* * *
29564313 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGCAATCG
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAGTCG
*
29564351 TGATATCCGGGTTAAG
1 T-ATATCCGGGCTAAG
29564367 TCCGTAGGCC
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 18 0.23
40 58 0.73
41 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (38 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAGTCG
Found at i:29568473 original size:40 final size:40
Alignment explanation
Indices: 29568428--29568635 Score: 229
Period size: 40 Copynumber: 5.2 Consensus size: 40
29568418 CGGAATACAA
*
29568428 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* * *
29568468 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* *
29568508 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* ** * *
29568548 CCGGATGTAGTCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTTGCACGAA-TGCCTTCGGGTCTTAGC
** * ** * * *
29568588 CCGGATATAATTACTAGCATAAATGTCTTTGGGACTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
29568628 CCGGATAT
1 CCGGATAT
29568636 CATTCAATTG
Statistics
Matches: 144, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
39 2 0.01
40 140 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:29578102 original size:42 final size:44
Alignment explanation
Indices: 29578032--29578141 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 44
29578022 TCTTACATGT
* *
29578032 AATCAAATATCGATGCCACTGTCTCAGACAAGGTCATACACG-A
1 AATCAAATATCGATGCCAATGTCCCAGACAAGGTCATACACGTA
* * *
29578075 AATCATATA-CGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 AATCAAATATCGATGCCAATGTCCCAGACAAGGTCATACACGTA
* * *
29578118 AATCACAGATCGATGCCAACGTCC
1 AATCAAATATCGATGCCAATGTCC
29578142 TAGATATGGT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 28 0.49
43 16 0.28
44 13 0.23
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (44 bp):
AATCAAATATCGATGCCAATGTCCCAGACAAGGTCATACACGTA
Found at i:29579988 original size:60 final size:59
Alignment explanation
Indices: 29579840--29579959 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 59
29579830 CTATTCAGAA
* * * *
29579840 ATCAGAGT-TAACTGGACCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAG
1 ATCAGAGTAT-ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAACCCATTACAG
*
29579900 TATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTTGGCCATAACCCTATTACA
1 -ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAACCC-ATTACA
29579960 AGTCGAGATA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 31 0.60
61 20 0.38
62 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (59 bp):
ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAACCCATTACAG
Found at i:29583564 original size:20 final size:20
Alignment explanation
Indices: 29583539--29583607 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
29583529 CCTAGATATA
29583539 TTTATGTGTGATTGTAGATT
1 TTTATGTGTGATTGTAGATT
** **
29583559 TTTATGAATCG-TCCCTAGATAT
1 TTTATGTGT-GAT-TGTAGAT-T
29583581 ATTTATGTGTGATTGTAGATT
1 -TTTATGTGTGATTGTAGATT
29583602 TTTATG
1 TTTATG
29583608 AATAGGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 14 0.39
21 7 0.19
22 7 0.19
23 8 0.22
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (20 bp):
TTTATGTGTGATTGTAGATT
Found at i:29583589 original size:43 final size:43
Alignment explanation
Indices: 29583528--29583610 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
29583518 GTGCTTTAAG
29583528 CCCTAGATATATTTATGTGTGATTGTAGATTTTTATGAATCGT
1 CCCTAGATATATTTATGTGTGATTGTAGATTTTTATGAATCGT
29583571 CCCTAGATATATTTATGTGTGATTGTAGATTTTTATGAAT
1 CCCTAGATATATTTATGTGTGATTGTAGATTTTTATGAAT
29583611 AGGTTAACTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (43 bp):
CCCTAGATATATTTATGTGTGATTGTAGATTTTTATGAATCGT
Found at i:29586429 original size:20 final size:23
Alignment explanation
Indices: 29586404--29586453 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 23
29586394 GGCATCTATG
29586404 TGTTCACAC-AATA-A-TAAAAA
1 TGTTCACACTAATATATTAAAAA
29586424 TGTTCACACTAATATATTAAAAA
1 TGTTCACACTAATATATTAAAAA
29586447 TGGTTCA
1 T-GTTCA
29586454 TGAATTCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.35
21 4 0.15
22 1 0.04
23 7 0.27
24 5 0.19
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (23 bp):
TGTTCACACTAATATATTAAAAA
Found at i:29588672 original size:28 final size:28
Alignment explanation
Indices: 29588636--29588744 Score: 148
Period size: 28 Copynumber: 3.9 Consensus size: 28
29588626 CTGCCAGAAT
* * *
29588636 AGAT-ATTGTGACAGAGTCACCAGATAC
1 AGATAATTGTGGCAGAGCCACCAGAAAC
* *
29588663 AGATAATTGTGGCAGGGCCACTAGAAAC
1 AGATAATTGTGGCAGAGCCACCAGAAAC
*
29588691 AGATATTTGTGGCAGAGCCACCAGAAAC
1 AGATAATTGTGGCAGAGCCACCAGAAAC
*
29588719 AGATATTTGTGGCAGAGCCACCAGAA
1 AGATAATTGTGGCAGAGCCACCAGAA
29588745 CGCTTCCTCC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 4 0.05
28 69 0.95
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (28 bp):
AGATAATTGTGGCAGAGCCACCAGAAAC
Found at i:29595973 original size:25 final size:25
Alignment explanation
Indices: 29595944--29595991 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29595934 TTATAATATG
* * *
29595944 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
29595969 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
29595992 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:29596060 original size:20 final size:20
Alignment explanation
Indices: 29596035--29596093 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
29596025 TAAATATGGT
29596035 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
29596055 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
29596075 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
29596094 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:29596075 original size:11 final size:11
Alignment explanation
Indices: 29596039--29596093 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
29596029 TATGGTATGT
29596039 ATGATATGCAC
1 ATGATATGCAC
* *
29596050 ATGAAATG--T
1 ATGATATGCAC
29596059 ATGATATGCAC
1 ATGATATGCAC
*
29596070 ATGATATG--T
1 ATGATATGCAC
29596079 ATGATATGCAC
1 ATGATATGCAC
29596090 ATGA
1 ATGA
29596094 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:29596188 original size:23 final size:24
Alignment explanation
Indices: 29596144--29596285 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
29596134 GAGGAAGTGA
29596144 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
29596168 AAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
29596191 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
29596214 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
29596238 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
29596262 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29596286 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
23 46 0.42
24 52 0.48
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:29596213 original size:47 final size:47
Alignment explanation
Indices: 29596144--29596285 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
29596134 GAGGAAGTGA
29596144 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
29596191 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
29596238 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
29596286 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
46 13 0.15
47 52 0.60
48 11 0.13
49 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:29596512 original size:31 final size:31
Alignment explanation
Indices: 29596477--29596568 Score: 154
Period size: 31 Copynumber: 3.1 Consensus size: 31
29596467 CGTTTACAGT
29596477 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29596508 AAAGGCTTCGGCCCAGT-A-AT-AAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
29596536 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29596567 AA
1 AA
29596569 TATGAAAAGG
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
28 25 0.44
29 2 0.04
30 3 0.05
31 27 0.47
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29604119 original size:25 final size:25
Alignment explanation
Indices: 29604090--29604137 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29604080 CCTTATAATG
* * *
29604090 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
29604115 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
29604138 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:29604206 original size:20 final size:20
Alignment explanation
Indices: 29604181--29604239 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
29604171 TAAATATGGT
29604181 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
29604201 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
29604221 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
29604240 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:29604221 original size:11 final size:11
Alignment explanation
Indices: 29604185--29604239 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
29604175 TATGGTATGT
29604185 ATGATATGCAC
1 ATGATATGCAC
* *
29604196 ATGAAATG--T
1 ATGATATGCAC
29604205 ATGATATGCAC
1 ATGATATGCAC
*
29604216 ATGATATG--T
1 ATGATATGCAC
29604225 ATGATATGCAC
1 ATGATATGCAC
29604236 ATGA
1 ATGA
29604240 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:29604334 original size:23 final size:24
Alignment explanation
Indices: 29604290--29604431 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
29604280 GAGGAAGTGA
29604290 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
29604314 AAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
29604337 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
29604360 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
29604384 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
29604408 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29604432 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
23 46 0.42
24 52 0.48
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:29604359 original size:47 final size:47
Alignment explanation
Indices: 29604290--29604431 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
29604280 GAGGAAGTGA
29604290 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
29604337 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
29604384 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
29604432 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
46 13 0.15
47 52 0.60
48 11 0.13
49 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:29604658 original size:31 final size:31
Alignment explanation
Indices: 29604623--29604717 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
29604613 CGTTTACAGT
29604623 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
29604654 AAAGGCTTCGGCCCAGTAATAAGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
29604685 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29604716 AA
1 AA
29604718 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29607872 original size:29 final size:29
Alignment explanation
Indices: 29607830--29607911 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
29607820 ATTATTTTTT
29607830 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
29607859 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
*
29607888 TTTCCAGCACGCACACTTAGTGCC
1 TTTCCAGCATGCACACTTAGTGCC
29607912 TATCTCGTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:29615777 original size:29 final size:29
Alignment explanation
Indices: 29615735--29615816 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
29615725 TTATTTTTTT
29615735 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
29615764 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
*
29615793 TTTCCAGCACGCACACTTAGTGCC
1 TTTCCAGCATGCACACTTAGTGCC
29615817 TATCTCGTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:29618740 original size:28 final size:28
Alignment explanation
Indices: 29618685--29618801 Score: 150
Period size: 28 Copynumber: 4.3 Consensus size: 28
29618675 AGCATGGCTG
*
29618685 CCAG-AACAGAT-ATTGTGACAGAGTCA
1 CCAGAAACAGATAATTGTGACAGAGCCA
* * *
29618711 CCAGACACAGATAATTGTGGCAGGGCCA
1 CCAGAAACAGATAATTGTGACAGAGCCA
* *
29618739 CCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATAATTGTGACAGAGCCA
*
29618767 CCAGAAACAGATATTTGTGACAGAGCCA
1 CCAGAAACAGATAATTGTGACAGAGCCA
29618795 CCA-AAAC
1 CCAGAAAC
29618802 GCTTCCTCCA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
26 4 0.05
27 10 0.12
28 67 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (28 bp):
CCAGAAACAGATAATTGTGACAGAGCCA
Found at i:29621941 original size:29 final size:28
Alignment explanation
Indices: 29621870--29621961 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
29621860 AGGTCTACAT
* *
29621870 ACATGCATATGGCCCACTAGGCCCAATC
1 ACATTCATATGGCCCATTAGGCCCAATC
* * *
29621898 TCGTTCAAATGGCCCATTAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAA-TC
*
29621927 ACATTCATATGGCCCATTAGGGCCAATC
1 ACATTCATATGGCCCATTAGGCCCAATC
*
29621955 ACTTTCA
1 ACATTCA
29621962 AAGTCATGCT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 29 0.55
29 24 0.45
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (28 bp):
ACATTCATATGGCCCATTAGGCCCAATC
Found at i:29622981 original size:4 final size:4
Alignment explanation
Indices: 29622974--29623004 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
29622964 TATATACTAA
*
29622974 AAAT AAAT AAAT AAAT ACAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
29623005 AATATAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:29632943 original size:29 final size:28
Alignment explanation
Indices: 29632906--29632978 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 28
29632896 AATGTCACTG
*
29632906 GGCCTAATGGGCCATATAAATGTGATTTT
1 GGCCTAATGGGCCATATAAAGGTGA-TTT
*
29632935 GGCCTAATGGGCCATATACAGGTGATTT
1 GGCCTAATGGGCCATATAAAGGTGATTT
*
29632963 GGACCTTATGGGCCAT
1 GG-CCTAATGGGCCAT
29632979 GTGAATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (28 bp):
GGCCTAATGGGCCATATAAAGGTGATTT
Found at i:29633920 original size:21 final size:21
Alignment explanation
Indices: 29633876--29633920 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29633866 TTTCATTATG
*
29633876 TTATTATTACTTGAATTATTA
1 TTATTATTACTTGAATTATAA
* * *
29633897 TTATTATTATTTTAATTGTAA
1 TTATTATTACTTGAATTATAA
29633918 TTA
1 TTA
29633921 CGAGAAGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TTATTATTACTTGAATTATAA
Found at i:29643017 original size:8 final size:8
Alignment explanation
Indices: 29643004--29643052 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
29642994 ATCGGCAAAA
29643004 GCCGAAAT
1 GCCGAAAT
29643012 GCCGAAAT
1 GCCGAAAT
29643020 GCCGAAAT
1 GCCGAAAT
***
29643028 GTTAAAAT
1 GCCGAAAT
*
29643036 GCCGAAAA
1 GCCGAAAT
*
29643044 GACGAAAT
1 GCCGAAAT
29643052 G
1 G
29643053 ACAAAAAGTC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (8 bp):
GCCGAAAT
Found at i:29643058 original size:24 final size:24
Alignment explanation
Indices: 29643008--29643058 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
29642998 GCAAAAGCCG
* * **
29643008 AAATGCCGAAATGCCGAAATGTTA
1 AAATGCCGAAAAGACGAAATGACA
29643032 AAATGCCGAAAAGACGAAATGACA
1 AAATGCCGAAAAGACGAAATGACA
29643056 AAA
1 AAA
29643059 AGTCGAAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.14
Consensus pattern (24 bp):
AAATGCCGAAAAGACGAAATGACA
Found at i:29643325 original size:29 final size:29
Alignment explanation
Indices: 29643282--29643420 Score: 169
Period size: 29 Copynumber: 4.9 Consensus size: 29
29643272 CATGAAAATG
* *
29643282 AATGTGA-CTGGGCCTAACGGGCCATATA
1 AATGTGATTTGGGCCTAATGGGCCATATA
29643310 AATGTGATTTGGGCCTAATGGGCCATATA
1 AATGTGATTTGGGCCTAATGGGCCATATA
*
29643339 CA-GATGATTTGGGCCTAATGGGCCATATA
1 AATG-TGATTTGGGCCTAATGGGCCATATA
* * *
29643368 CAGGTGATTTGGGCCTAATGGGCCATATG
1 AATGTGATTTGGGCCTAATGGGCCATATA
*
29643397 AATATGA-TTGGG-CTAAATGGGCCA
1 AATGTGATTTGGGCCT-AATGGGCCA
29643421 GATATAGATA
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
27 2 0.02
28 22 0.22
29 75 0.75
30 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAATGGGCCATATA
Found at i:29645509 original size:40 final size:40
Alignment explanation
Indices: 29645443--29645609 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
29645433 AAATTGAATG
* * *
29645443 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
29645482 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
29645522 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
29645562 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
29645602 ATATCCGG
1 ATATCCGG
29645610 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:29648301 original size:40 final size:40
Alignment explanation
Indices: 29648238--29648404 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
29648228 CATTTGAATG
* * * *
29648238 ATATCCGGGCTAAGTCCCAAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
29648278 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * **
29648318 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * * *
29648358 AAATCCGGGTTAGGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
29648398 ATATCCG
1 ATATCCG
29648405 ATTAAATCCC
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.03
40 96 0.92
41 5 0.05
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:29650603 original size:34 final size:34
Alignment explanation
Indices: 29650509--29650591 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 34
29650499 CTGATATGTT
*
29650509 AATGGGCTTAGGCCCAGACTGCTACTGTTACTGA
1 AATGGGCTAAGGCCCAGACTGCTACTGTTACTGA
*
29650543 AATGGGCTCAA-GCCCAGATTGCTACTGTTACTGA
1 AATGGGCT-AAGGCCCAGACTGCTACTGTTACTGA
*
29650577 AATTGGCTAAGGCCC
1 AATGGGCTAAGGCCC
29650592 TAGCTGTTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 2 0.05
34 41 0.93
35 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (34 bp):
AATGGGCTAAGGCCCAGACTGCTACTGTTACTGA
Found at i:29653952 original size:27 final size:27
Alignment explanation
Indices: 29653922--29654187 Score: 352
Period size: 27 Copynumber: 9.9 Consensus size: 27
29653912 TTAACCATAG
* *
29653922 AGGGGTATTACGGTCATTTTATCCTAC
1 AGGGGCATTACGGTCATTTTACCCTAC
*
29653949 AGGGGCATTACGGTCATTTTATCCTAC
1 AGGGGCATTACGGTCATTTTACCCTAC
29653976 AGGGGCATTACGGTCATTTTACCCTAC
1 AGGGGCATTACGGTCATTTTACCCTAC
* ** * * *
29654003 AAGGATATTACGATCATTTTACTCTAT
1 AGGGGCATTACGGTCATTTTACCCTAC
*
29654030 AGGGGCATTACGGTCATTTTACCCTAT
1 AGGGGCATTACGGTCATTTTACCCTAC
* *
29654057 AGGGGCATTACGATTATTTTACCCTAC
1 AGGGGCATTACGGTCATTTTACCCTAC
* **
29654084 AGGGGTATTGTGGTCATTTTACCCTAC
1 AGGGGCATTACGGTCATTTTACCCTAC
*
29654111 AGGGGCATTACGGTCATTTTACCCTAT
1 AGGGGCATTACGGTCATTTTACCCTAC
* * *
29654138 AGGGGAATTGCGGTTATTTTACCCTAC
1 AGGGGCATTACGGTCATTTTACCCTAC
*
29654165 AGGGGCATTATGGTCATTTTACC
1 AGGGGCATTACGGTCATTTTACC
29654188 TATTTTAGGG
Statistics
Matches: 206, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 206 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (27 bp):
AGGGGCATTACGGTCATTTTACCCTAC
Found at i:29654187 original size:81 final size:81
Alignment explanation
Indices: 29653908--29654187 Score: 389
Period size: 81 Copynumber: 3.5 Consensus size: 81
29653898 GGCATAATCA
* * * * *
29653908 TTATTTAACCATAGAGGGGTATTACGGTCATTTTATCCTACAGGGGCATTACGGTCATTTTATCC
1 TTATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCC
*
29653973 TACAGGGGCATTACGG
66 TATAGGGGCATTACGG
* * * * * *
29653989 TCATTTTACCCTACAAGGATATTACGATCATTTTACTCTATAGGGGCATTACGGTCATTTTACCC
1 TTATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCC
*
29654054 TATAGGGGCATTACGA
66 TATAGGGGCATTACGG
**
29654070 TTATTTTACCCTACAGGGGTATTGTGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCC
1 TTATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCC
* *
29654135 TATAGGGGAATTGCGG
66 TATAGGGGCATTACGG
* *
29654151 TTATTTTACCCTACAGGGGCATTATGGTCATTTTACC
1 TTATTTTACCCTACAGGGGTATTACGGTCATTTTACC
29654188 TATTTTAGGG
Statistics
Matches: 173, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 173 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (81 bp):
TTATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCC
TATAGGGGCATTACGG
Found at i:29665504 original size:42 final size:41
Alignment explanation
Indices: 29665368--29665504 Score: 125
Period size: 42 Copynumber: 3.3 Consensus size: 41
29665358 CATACCAATG
* * * *
29665368 CCATATCCCAGATATGGTCTTACATCGGATCTCATATCGATTC
1 CCATATCCCAGACATGGTCTTACA-CGAATCTCATAACGA-TA
* * ** *
29665411 CCATA-GCCAG-CTATGGTCTTACACGATTCTCATATTGATG
1 CCATATCCCAGAC-ATGGTCTTACACGAATCTCATAACGATA
* *
29665451 CCATGTGCCAGACATGGTCTTACACGAAATCTCATAACGATA
1 CCATATCCCAGACATGGTCTTACACG-AATCTCATAACGATA
29665493 CCATATCCCAGA
1 CCATATCCCAGA
29665505 TATTTTCTTA
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
40 5 0.06
41 30 0.39
42 37 0.48
43 5 0.06
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (41 bp):
CCATATCCCAGACATGGTCTTACACGAATCTCATAACGATA
Found at i:29665514 original size:83 final size:83
Alignment explanation
Indices: 29665365--29665517 Score: 184
Period size: 83 Copynumber: 1.8 Consensus size: 83
29665355 AATCATACCA
* * * * * *
29665365 ATGCCATATCCCAGATATGGTCTTACATCGGATCTCATATCGATTCCCATAGCCAGCTATGGTCT
1 ATGCCATATCCCAGACATGGTCTTACATCGAATCTCATAACGATTACCATACCCAGATATGGTCT
29665430 TACACGATTCTCATATTG
66 TACACGATTCTCATATTG
* * **
29665448 ATGCCATGTGCCAGACATGGTCTTACA-CGAAATCTCATAACGA-TACCATATCCCAGATATTTT
1 ATGCCATATCCCAGACATGGTCTTACATCG-AATCTCATAACGATTACCATA-CCCAGATATGGT
29665511 CTTACAC
64 CTTACAC
29665518 ATAAACTCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
82 8 0.14
83 50 0.86
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (83 bp):
ATGCCATATCCCAGACATGGTCTTACATCGAATCTCATAACGATTACCATACCCAGATATGGTCT
TACACGATTCTCATATTG
Found at i:29677857 original size:46 final size:45
Alignment explanation
Indices: 29677790--29677964 Score: 199
Period size: 46 Copynumber: 3.8 Consensus size: 45
29677780 TGTAACCCGC
*
29677790 CCATAAGTGAACTCGGACTCAACTTAACGAGCTCAGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGTGTTCGCAT
* * *
29677836 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-TG-TTCGCAT
* *** * *
29677882 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGTCATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGT-GTTCGCAT
*
29677929 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
29677965 ATGCCCAAAT
Statistics
Matches: 107, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
45 2 0.02
46 71 0.66
47 34 0.32
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGTGTTCGCAT
Found at i:29677957 original size:93 final size:93
Alignment explanation
Indices: 29677798--29677969 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
29677788 GCCCATAAGT
* *
29677798 GAACTCGGACTCAACTTAACGAGCTCAGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGGTATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29677863 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
29677891 GAACTCGGACTCAACTCAACGAGTTC-GGTCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCAGGT-ATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
29677955 ACGAGTTCGGATGCC
65 ACGAGCTCGGATGCC
29677970 CAAATATCCC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 3 0.04
93 71 0.96
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGGTATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:29680796 original size:30 final size:30
Alignment explanation
Indices: 29680762--29680893 Score: 156
Period size: 30 Copynumber: 4.4 Consensus size: 30
29680752 AGCTATCCAT
*
29680762 TTTTCATAATTTGATGGTCTTCACCATCCC
1 TTTTCATAATTTGATGGTCGTCACCATCCC
** * * **
29680792 TTTTCATTGTTCGATGGTCGTCATCATTGC
1 TTTTCATAATTTGATGGTCGTCACCATCCC
* * *
29680822 TTTTCACAATTTGATGGTTGTCATCATCCC
1 TTTTCATAATTTGATGGTCGTCACCATCCC
* *
29680852 TTTTCATAATTTGATGGTGGTCACCATCCT
1 TTTTCATAATTTGATGGTCGTCACCATCCC
29680882 TTTTCATAATTT
1 TTTTCATAATTT
29680894 ATAGCTGAAG
Statistics
Matches: 84, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (30 bp):
TTTTCATAATTTGATGGTCGTCACCATCCC
Found at i:29685999 original size:217 final size:217
Alignment explanation
Indices: 29685624--29686032 Score: 764
Period size: 217 Copynumber: 1.9 Consensus size: 217
29685614 ACATTACTTC
29685624 AAAGTTATAGCCTCAAATCGTCATCTTCTTCATCACTTAAAAAGCCGAAATACCATGGATTTAGA
1 AAAGTTATAGCCTCAAATCGTCATCTTCTTCATCACTTAAAAAGCCGAAATACCATGGATTTAGA
*
29685689 GACTTATAGCCGAAACTTCAGATCTCCTGGATTCGAGTTCTACTATCATTTAGAGGATAGATCTG
66 GACTTATAGCCGAAACTTCAGATCTCCTGGATTCAAGTTCTACTATCATTTAGAGGATAGATCTG
29685754 CATCAGATCTGCATAGAAATCAAAGAGGAATAAGTGGTAAGTGCTCATCACCTCAGATCTAGTCT
131 CATCAGATCTGCATAGAAATCAAAGAGGAATAAGTGGTAAGTGCTCATCACCTCAGATCTAGTCT
29685819 TATTTTACAATTTAGAAAAGGT
196 TATTTTACAATTTAGAAAAGGT
*
29685841 AAAGTTATAGCCTCAAATCGTCATCTTCTTCATCACTTAAAAAGCCGAAATACCATGGATTTAGG
1 AAAGTTATAGCCTCAAATCGTCATCTTCTTCATCACTTAAAAAGCCGAAATACCATGGATTTAGA
** *
29685906 GACTTATAGTTGAAACTTCAGATCTCCTGGATTCAAGTTCTACTATCGTTTAGAGGATAGATCTG
66 GACTTATAGCCGAAACTTCAGATCTCCTGGATTCAAGTTCTACTATCATTTAGAGGATAGATCTG
*
29685971 CATCAGATCTGCGTAGAAATCAAAGAGGAATAAGTGGTAAGTGCTCATCACCTCAGATCTAG
131 CATCAGATCTGCATAGAAATCAAAGAGGAATAAGTGGTAAGTGCTCATCACCTCAGATCTAG
29686033 GTAGGTTGTC
Statistics
Matches: 186, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
217 186 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (217 bp):
AAAGTTATAGCCTCAAATCGTCATCTTCTTCATCACTTAAAAAGCCGAAATACCATGGATTTAGA
GACTTATAGCCGAAACTTCAGATCTCCTGGATTCAAGTTCTACTATCATTTAGAGGATAGATCTG
CATCAGATCTGCATAGAAATCAAAGAGGAATAAGTGGTAAGTGCTCATCACCTCAGATCTAGTCT
TATTTTACAATTTAGAAAAGGT
Found at i:29688444 original size:30 final size:31
Alignment explanation
Indices: 29688410--29688468 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
29688400 ATCTAATATG
*
29688410 AACTTTGGCAAAATTACA-TTTTTGCCCTTA
1 AACTTTGGCAAAATTACACTTTTTCCCCTTA
* *
29688440 AACTTTTGCATAATTACACTTTTTCCCCT
1 AACTTTGGCAAAATTACACTTTTTCCCCT
29688469 AGGCTCGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (31 bp):
AACTTTGGCAAAATTACACTTTTTCCCCTTA
Found at i:29689609 original size:34 final size:34
Alignment explanation
Indices: 29689571--29689672 Score: 161
Period size: 34 Copynumber: 3.0 Consensus size: 34
29689561 CAATGATATG
29689571 GTACATCTCAAGCAATCATCTTAATGACACAACA
1 GTACATCTCAAGCAATCATCTTAATGACACAACA
** *
29689605 GTACATCTCAAGCAATCATCTGGATGACACAATA
1 GTACATCTCAAGCAATCATCTTAATGACACAACA
29689639 GTACATCTCAAGCAATCAT-TTAGATGACACAACA
1 GTACATCTCAAGCAATCATCTTA-ATGACACAACA
29689673 TCTCGTCTAG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 1 0.02
34 60 0.98
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.24
Consensus pattern (34 bp):
GTACATCTCAAGCAATCATCTTAATGACACAACA
Found at i:29693535 original size:78 final size:78
Alignment explanation
Indices: 29693427--29693571 Score: 211
Period size: 78 Copynumber: 1.9 Consensus size: 78
29693417 TAGATCAAAA
* * *
29693427 CTCATATAATCACATAACATTCAAGCATATATCACGATATACATTTAATCTTC-TAACATTTAAG
1 CTCATATAATCACATAACATTCAAGCATATACCACAATATACATATAATC-TCATAACATTTAAG
29693491 CATGTATTACAACT
65 CATGTATTACAACT
* * * *
29693505 CTCATATAGTCACATTACATTCAAGCATATACCACAATATAGATATAATCTCATAACGTTTAAGC
1 CTCATATAATCACATAACATTCAAGCATATACCACAATATACATATAATCTCATAACATTTAAGC
29693570 AT
66 AT
29693572 ATCACAATAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 2 0.03
78 57 0.97
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (78 bp):
CTCATATAATCACATAACATTCAAGCATATACCACAATATACATATAATCTCATAACATTTAAGC
ATGTATTACAACT
Found at i:29693570 original size:39 final size:39
Alignment explanation
Indices: 29693373--29693580 Score: 137
Period size: 39 Copynumber: 5.4 Consensus size: 39
29693363 ATTCACTTTT
* * *
29693373 AAGCATATATC-CTATTACACATTTAATCACCA-AACATTC
1 AAGCATATATCAC-AATATACATATAATCA-CATAACATTC
* *
29693412 AAACATAGATCA-AA-ACT-CATATAATCACATAACATTC
1 AAGCATATATCACAATA-TACATATAATCACATAACATTC
* * * *
29693449 AAGCATATATCACGATATACATTTAATCTTC-TAACATTT
1 AAGCATATATCACAATATACATATAATC-ACATAACATTC
* * * * *
29693488 AAGCATGTATTACAACTCT-CATATAGTCACATTACATTC
1 AAGCATATATCACAA-TATACATATAATCACATAACATTC
* * * * *
29693527 AAGCATATACCACAATATAGATATAATCTCATAACGTTT
1 AAGCATATATCACAATATACATATAATCACATAACATTC
29693566 AAGC--ATATCACAATA
1 AAGCATATATCACAATA
29693581 CTCAAAAACA
Statistics
Matches: 128, Mismatches: 31, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
36 2 0.02
37 37 0.29
38 6 0.05
39 80 0.62
40 3 0.02
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (39 bp):
AAGCATATATCACAATATACATATAATCACATAACATTC
Done.